The content of the video stream is unrelated to the chrome key value; the video stream can never cause itself to be shown/hidden.

The chroma key value (i.e. presentation queue background color) is a color painted into the desktop surface (i.e. drawn into the presentation queue target window) that will cause the video to show up.

The only possible issue with chroma keying is: If some other window (i.e. not the presentation queue target) is moved over the top of the presentation queue target window, then that other window should be completely visible and occlude the presentation queue target entirely. However, if that other window is painted (or partially painted) the same color as the chroma key, then video may show over that window instead of being occluded.